2BDP
CRYSTAL STRUCTURE OF BACILLUS DNA POLYMERASE I FRAGMENT COMPLEXED TO 9 BASE PAIRS OF DUPLEX DNA
X-RAY DIFFRACTION
Crystallization
Crystalization Experiments | ||||
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ID | Method | pH | Temperature | Details |
1 | VAPOR DIFFUSION, HANGING DROP | 5.8 | pH 5.8, VAPOR DIFFUSION, HANGING DROP |
Crystal Properties | |
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Matthews coefficient | Solvent content |
2.96 | 58.46 |
Crystal Data
Unit Cell | |
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Length ( ? ) | Angle ( ? ) |
a = 86.241 | ¦Á = 90 |
b = 93.275 | ¦Â = 90 |
c = 106.374 | ¦Ã = 90 |
Symmetry | |
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Space Group | P 21 21 21 |
Diffraction
Diffraction Experiment | ||||||||||||||
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ID # | Crystal ID | Scattering Type | Data Collection Temperature | Detector | Detector Type | Details | Collection Date | Monochromator | Protocol | |||||
1 | 1 | x-ray | 90 | IMAGE PLATE | RIGAKU RAXIS IIC | 1997-03-15 | M |
Radiation Source | |||||
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ID # | Source | Type | Wavelength List | Synchrotron Site | Beamline |
1 |
Data Collection
Overall | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (Observed) | R Sym I (Observed) | Net I Over Average Sigma (I) | Redundancy | Number Reflections (All) | Number Reflections (Observed) | Observed Criterion Sigma (F) | Observed Criterion Sigma (I) | B (Isotropic) From Wilson Plot | ||||||||
1 | 1.8 | 20 | 91.7 | 0.044 | 3.4 | 73375 | 73375 | 22.1 |
Highest Resolution Shell | |||||||||||||||||||
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ID # | Resolution (High) | Resolution (Low) | Percent Possible (All) | Percent Possible (Observed) | R-Sym I (Observed) | Mean I Over Sigma (Observed) | Redundancy | Number Unique Reflections (All) | |||||||||||
1.8 | 1.83 | 60.1 | 0.163 |
Refinement
Statistics | |||||||||||||||||||
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Diffraction ID | Structure Solution Method | Cross Validation method | Starting model | Resolution (High) | Resolution (Low) | Number Reflections (All) | Number Reflections (Observed) | Number Reflections (R-Free) | Percent Reflections (Observed) | R-Factor (Observed) | R-Work | R-Free | R-Free Selection Details | Mean Isotropic B | |||||
X-RAY DIFFRACTION | MOLECULAR REPLACEMENT | THROUGHOUT | UNPUBLISHED DNA COMPLEX STRUCTURE | 1.8 | 20 | 73281 | 73281 | 3701 | 87 | 0.241 | 0.241 | 0.276 | RANDOM | 19.8 |
Temperature Factor Modeling | ||||||
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Anisotropic B[1][1] | Anisotropic B[1][2] | Anisotropic B[1][3] | Anisotropic B[2][2] | Anisotropic B[2][3] | Anisotropic B[3][3] | |
0.3 | -0.25 | -0.05 |
RMS Deviations | |
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Key | Refinement Restraint Deviation |
x_dihedral_angle_d | 24.8 |
x_scangle_it | 2.66 |
x_scbond_it | 1.65 |
x_angle_deg | 1.4 |
x_mcangle_it | 1.35 |
x_improper_angle_d | 1.02 |
x_mcbond_it | 0.82 |
x_bond_d | 0.01 |
x_bond_d_na | |
x_bond_d_prot |
Non-Hydrogen Atoms Used in Refinement | |
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Non-Hydrogen Atoms | Number |
Protein Atoms | 4656 |
Nucleic Acid Atoms | 387 |
Solvent Atoms | 468 |
Heterogen Atoms | 16 |
Software
Software | |
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Software Name | Purpose |
X-PLOR | model building |
X-PLOR | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
X-PLOR | phasing |